Mark Rossetti, the once-feared captain of the New England Mafia, appeared before a Suffolk Superior Court judge in jogging pants and handcuffs Friday and was sentenced to 12 years in prison, effectively punctuating a sweeping case that charged him with running a violent criminal enterprise across Eastern Massachusetts.

Rossetti, now 53 and silver-haired, had a controversial secret relationship with the FBI. He had pleaded guilty to usury and extortion, to lending money at exorbitant interest rates to a gambler, and to using threats to collect gambling debts for bookies.

He will serve the sentence concurrently with sentences for recent convictions of selling ­heroin and of breaking and entering to rob a ­rival drug dealer.

With the sentence Friday, the third and final punishment stemming from an indictment in 2010, Rossetti is sure to remain in prison until he is in his 60s, the latest blow to La Cosa ­Nostra in New England.

“Mark Rossetti was the leader of an extensive and violent criminal enterprise that for ­decades threatened the safety of our community,” said Attorney General Martha Coakley, whose office sought indictments of Rossetti and about 30 other Mafia members and associates in October 2010 for running a vast enterprise known as the Rossetti organization.

“This sentence today is an important step in our efforts to combat organized crime,” Coakley said, adding that “Rossetti and many of his asso­ciates have been taken off our streets and are no longer threats to public safety.”

Rossetti, after telling Superior Court Judge Jeffrey A. Locke that he worked in construction and never went past the ninth grade, said he understood the charges and his decision to plead guilty.

His attorney, Michael Doolin, said that his client was glad to resolve the case and “looks forward to putting these ­issues behind him and getting on in his life.”

Rossetti has a history of convictions, for robbing an armored vehicle and having guns, and he once chose to serve jail time rather than testify about organized crime. He had been identified by State Police as a suspect in several murders.

But the indictment of him and his associates in 2010 after an investigation initiated by Essex County authorities and the State Police also helped to expose his secret work for the FBI as a federal informant, a questionable relationship, given his history of crime and his continuing role as a Mafia leader. The FBI had enacted guidelines banning similar relationships in the wake of its corrupt handling of James “Whitey” Bulger.

The FBI said after the relationship with Rossetti was exposed in court records that it had ended its work with the Mafioso once it realized he had been engaging in organized crime and that it assisted with the State Police inquiry. The bureau has admitted to no wrongdoing and said it is conducting an internal review of the relationship.

Several of Rossetti’s associates sought dismissal of their cases, arguing they could not be convicted for conspiring with Rossetti because he had been a government informant, but their requests were denied.

A recent tally showed that nearly 20 of ­Rossetti’s associates have been convicted and are serving either prison terms or probation for a variety of crimes, including gambling, bookmaking, loansharking, drug dealing, and extortion

Assistant Attorney General Dean Mazzone had asked Locke for the 12-year prison sentence for Rossetti, citing his history as a Mafia leader.

“His record is a horrendous one,” Mazzone said. “The defendant was a capo in the Boston area Mafia. He directed various crimes over the course of several years.”